Pearl was kidnapped on 23 January, 2002, in the southern Pakistan city of Karachi while working on a story on "Islamic militancy", and was later killed in captivity.
Malik Tasaddaq, 28, was arrested in the eastern Punjab province on suspicion of involvement in Pearl's killing, the province's police chief Saadat Allah Khan said in a statement on Friday.
Tasaddaq and Nadir Khan, who was detained in a separate raid in Punjab, allegedly belong to Lashkar-e-Jhangvi, an outlawed Sunni Muslim group blamed for attacks on minority Shia, Westerners and the government, the statement said.
Khan, 30, was wanted for his alleged role in the killing of a police official and a Shia Muslim leader.
Four Islamist fighters have been convicted of kidnapping Pearl, but seven other suspects - including those who allegedly slit his throat in front of a video camera - remain at large.
In August 2001, President Pervez Musharraf banned Lashkar-e-Jhangvi, which was linked to the Taliban militia in Afghanistan, in a crackdown aimed at eliminating religious extremism in the country.
Khan and Tasaddaq each carried a reward of one million rupees (US$17,000) for information leading to their arrest.